NM_003647.3:c.59G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003647.3(DGKE):c.59G>A(p.Gly20Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00232 in 1,612,018 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003647.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0129 AC: 1964AN: 152244Hom.: 31 Cov.: 33
GnomAD3 exomes AF: 0.00337 AC: 838AN: 248394Hom.: 23 AF XY: 0.00250 AC XY: 337AN XY: 134674
GnomAD4 exome AF: 0.00121 AC: 1773AN: 1459656Hom.: 39 Cov.: 31 AF XY: 0.00102 AC XY: 744AN XY: 725932
GnomAD4 genome AF: 0.0129 AC: 1971AN: 152362Hom.: 31 Cov.: 33 AF XY: 0.0127 AC XY: 949AN XY: 74506
ClinVar
Submissions by phenotype
not provided Benign:3
This variant is associated with the following publications: (PMID: 29440240) -
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Kidney disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at